ADL: reference RMSD

Dario Ghersi dario.ghersi at
Wed Jan 30 11:42:10 PST 2008

Yes, thank you very much for the explanation. I actually found out  
that it's possible to choose whether to match with the closest atom of  
the same type or with the corresponding one in the reference by using  
the keyword 'rmsnosym'.

Thanks and best regards,


On Jan 30, 2008, at 1:36 PM, Ruth Huey wrote:

> Dario Ghersi wrote:
>> Dear all,
>> I have a problem with the reference RMSD that's reported in the .dlg
>> file.
>> If I compare that value with the one that comes out of
>> I get different values (sometimes the  
>> difference
>> is > 2.0A). I also calculated the RMSD separately with my script and
>> the results are consistent with
>> So I was wondering how the reference RMSD is actually calculated in
>> the .dlg file.
>> Thank you very much,
>> Dario Ghersi
>> ________________________________________________
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> In the .dlg file, the rmsd calculation matches each atom in the docked
> structure with the closest one of the same atom type in the reference
> structure.
> The python script matches each atom in the docked structure with its
> position in the reference structure.
>   Ruth
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